Quantification of gene copy numbers is valuable in marine microbial ecology: A comment to Meiler et al. (2022)

Challenges and opportunities in connecting gene count observations with ocean biogeochemical models: Reply to Zehr and Riemann (2023)

“…As authors of Meiler et al (2022), we welcome Zehr and Riemann's (2023) comment and discussion. We agree, of course, with the general statement that “quantification of gene copy numbers is valuable in marine microbial ecology” and wish to clarify that one of the purposes of Meiler et al (2022) was to address the specific challenge of using a compilation of quantitative polymerase chain reaction (qPCR) nifH data to evaluate the skill of biogeochemical models.…”

“…Genes such as nifH form a minute and variable fraction of total biomass so to quantitatively interface gene densities and modeled biomass an intercalibration is required: either data must be re‐expressed as biomass, or modeled biomass must be related to gene densities (Coles et al 2017). Critically, as both Meiler et al (2022) and Zehr and Riemann (2023) discuss, this intercalibration requires knowledge of several factors including gene copies per cell, and biomass per cell, which are not yet well constrained. The intercalibration issue is not unique to gene densities (as also noted by Zehr and Riemann 2023): The synthesis of published biogeography compilations of several phytoplankton functional types, relying mostly on microscopy, faces similar issues (Buitenhuis et al 2013, and references therein) and uncertainty is also present in conversions between flow cytometry pico‐ and pico‐nano‐sized cell counts to biomass (Ribalet et al 2019).…”

“…Uncertainties in nifH genes‐per‐cell (influenced by polyploidy), as well as cell quotas, along with data aggregation, lead to wide ranges of uncertainty in the calibrations with implications for model testing. Zehr and Riemann (2023) argue that the study may lead readers to under‐value nifH gene density data, highlighting several specific concerns. In the following section we address those points and identify avenues for positive future action.…”

“…Meiler et al (2022) compiled published data on gene‐copies per cell for diazotrophs in order to facilitate the necessary intercalibration of abundances between gene‐counts and biomass. Zehr and Riemann (2023) point out that the compilation of Meiler et al (2022) was too small to constrain the calibration tightly. It did, however, reflect the published information available at the time.…”

“…In the following, we first provide a background perspective for the Meiler et al (2022) study, pointing out why observations and simulations are rooted in different currencies. We then discuss in more detail some of the specific points raised by Zehr and Riemann (2023) and highlight why further efforts toward intercalibration of currencies used to measure and simulate marine microbial populations is particularly significant if we are to fully exploit the data in biogeochemical and climate modeling applications. We end by summarizing some potentially fruitful avenues for future effort stimulated by this dialog.…”